Two of those held belong to the Southeast Asia-based Jemaah Islamiyah (JI) terror network and the third is a member of the Moro Islamic Liberation Front (MILF), an armed group waging an insurgency in the southern Philippines.
The three were detained under the Internal Security Act (ISA), which allows detention of suspects without trial.
A statement by the Ministry of Home Affairs said the suspects were arrested outside Singapore and were placed under ISA detention after they were deported to the city-state -- indicating the three are Singaporeans.
One of those being held is Samad bin Subari, a JI member who had "undergone terrorist training with al-Qaeda in Afghanistan in 2001", the statement said.
He had fled to Indonesia following a crackdown against the JI in Singapore and was arrested by Indonesian police in Sumatra in June 2009.
Samad was imprisoned in Indonesia for immigration offences and deported to Singapore after the completion of his sentence in June 2011.
The second suspect, Jumari bin Kamdi, is also a JI member who received military training organised by the terror group.
He was arrested in an unidentified neighbouring country late last year and deported to Singapore, the home ministry said.
The third suspect, Abdul Majid Kunji Mohammad, was trained in making improvised explosive devices at a MILF base on the southern Philippine island of Mindanao.
An MILF member since 1998, he had helped in "procuring funds and weapons components" for the insurgency. He was arrested in Malaysia in May and deported to Singapore.
Singapore launched a crackdown against the JI in 2001 and arrested several members suspected of planning bomb attacks against American and other foreign targets in the city-state.
Officials and analysts say the country remains a likely target for terror groups because of the presence of thousands of multinational firms, its high-profile status as a regional financial centre and its strong ties with the United States.